Mercurial > repos > ecology > cb_div
diff div_index.xml @ 0:abc8da8c12ba draft
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
author | ecology |
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date | Wed, 04 Jan 2023 13:21:41 +0000 |
parents | |
children | 5b31641e6d30 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/div_index.xml Wed Jan 04 13:21:41 2023 +0000 @@ -0,0 +1,83 @@ +<tool id="cb_div" name="Diversity" version="@VERSION@" profile = "20.01"> + <description>indicators</description> + <macros> + <import>macro.xml</import> + </macros> + <expand macro="cb_requirements"> + <requirement type="package" version="1.3.2">r-tidyverse</requirement> + <requirement type="package" version="1.7_20">r-ade4</requirement> + <requirement type="package" version="2.2">r-adiv</requirement> + <requirement type="package" version="3.4.0">r-ggplot2</requirement> + </expand> + <required_files> + <include type="literal" path="div_index.r"/> + </required_files> + <command detect_errors="exit_code"><![CDATA[ + Rscript + '$__tool_directory__/div_index.r' + '$input_data' + '$output_div' + '$output_rdata' + '$plots' + ]]> + </command> + <inputs> + <param name="input_data" type="data" format="rdata" label="Input Clean data"/> + </inputs> + <outputs> + <data name="output_div" from_work_dir="Valeurs_stat.tabular" format="tabular" label="Diversity index"/> + <data name="output_rdata" from_work_dir="div_df.RDS" format="rdata" label="Diversity Rdata"/> + <collection type="list" name="plots" label="Diversity plot"> + <discover_datasets pattern="(?P<designation>.+)\.png" visible="false" format="png"/> + </collection> + </outputs> + <tests> + <test expect_num_outputs="3"> + <param name="input_data" value="Clean_Rdata.rdata"/> + <output name="output_div"> + <assert_contents> + <has_n_columns n="20"/> + </assert_contents> + </output> + <output name="output_rdata"> + <assert_contents> + <has_text text="no"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="14"/> + </test> + </tests> + <help><![CDATA[ +==================== +Diversity indicators +==================== + + +**What it does** + +Calculates the diversity indicators (Shannon, Simpson, ...). + +**Input description** + +Clean Rdata file from the previous tool Dissimilarity. + ++----------------+ +| Rdata | ++================+ +| Clean data | ++----------------+ +| ... | ++----------------+ + + +**Output** + +- 1 .RDS file +- 1 tabular file for all the diversity indices +- Multiple png plots one for each indices + + + + ]]> </help> + <expand macro="cb_bibref"/> +</tool>